VDSers, post new questions below this (just Login and Edit this page). Dr. B will then answer them below. This can by anonymous..
updated by Dr. B on 03/31/13 @ 10:21 PM
Q:
Q:
RESPONSES from Dr. B (or mentors)
Q19: On the analysis below each pair of images, what exactly do we need to discuss?
A: discuss the differences in the pose and the differences in estimated binding strength relative to what you see with regards to polar contacts and hydrophobic interactions. Also, state if it should be better or worse than the reference ligand (Folate #2)
Q18: Materials and Methods should be past tense right? A: yes. M&M is past tense. (and pretty much everything else - unless it is future directions or the objective at the end of the intro) Q17: When we need to site PyMol, GOLD, other instruments we used, do we need to always site the company, city, state/country every time it's mentioned or just the first time it's mentioned in our report?A: just the first time it is cited - usually in the M&M
Q16: Do we need figures 17 - 21 and 22/23 in our report? Those are decoy ligands and best/worst sets. They are not paired analysis of GOLD and x-ray data.
A: Yes - they are actually more interesting than the other images. Q15: When citing GOLD, what is meant by the "first citation listed"? Is that the first reference on the pdf link for GOLD?---->[1] G. Jones, P.Willett, R. C. Glen, J. Mol. Biol., 245, 43-53, 1995; G. Jones, P.Willett, R. C. Glen, A. R. Leach, R. Taylor, J. Mol. Biol., 267, 727-748, 1997. ??A: yes - be sure to use ACS format though. Q14: How can we group ligands that are similar in our analysis? Does this mean that we don"t have to talk about each pair of images after we show the pictures and just explain 4 images at once?A: Yes - it is permissible to talk about a 'set' of images if the ligand are very similar. The best case of this are the tautomers of deazafolate. They are very similar and can be discussed together for the analysis as to whether they match their crystal poses and whether they would be high affinity ligands based upon polar contacts and hydrophobic interactions. . But still need separate captions.
Q13: Does the introduction have to be around 500 words, because this takes up a large amount of the word limit? Is it okay if the introduction is around 300 words, so we can focus more on the analysis section?
A: It should be ~500 words. 400 is about as low as you should go.
Q14: I was wondering what "cite the PDB entry for your receptor" is asking for? A: You want to cite the actual paper that the crystal structure is from (not just the PDB website page). Go to the page to find the artilcle http://www.rcsb.org/pdb/explore.do?structureId=1u72 (HINT: it was published in 2005) You can then get the full citation from PubMed or EndNote Web Online.
Q12: Can we use the comparisons that are in our lab analysis for our comparisons in the lab report? I planned on taking the answers in the lab analysis and making them more succint for the lab report. Is that okay?
A: yes - use your comparisons from the lab notebook and make them more succinct. Also, some ligands are very similar and can be grouped together in your analysis.
Q11: Should we put the excel table of both runs in our report or just the first one?
A: no - you really only need the 1st table.
Q10: I just realized that there were articles in the DDFE folder that we needed to save and keep for the lab report. Is there any way those could be uploaded to blackboard or to the VDS website so we can access them?
A: download WinSCP or SecureShell (from Bevoware on Utexas.edu) and remotely login to the DDFE.
Q9: Do the captions need to be in past tense as well or is it acceptable to have sentences such as "active site residues are shown as lines" "carbons on DHFR are colored green"?
A: no - it is best to keep those in present tense. 'active site residues shown as lines...."
Q8: Do all of the Figures from our notebook go into our report? Or are all twenty something figures too many to put in a lab report?
A: yes of the images listed should go in there (show the xray vs gold images side by side)
Q7: Should we capitalize things like "virtual screening" and "fitness score"? What about "hydrogen bond"?
A: 'Fitness Score' can be capitalized.
Q6: Since there is no way we can actually quanitfy the level of precision or accuracy that GOLD had, do we just use general adjectives based on our opinion/analysis? In short, is there a "right" answer?
A: correct - this is a more qualitative analysis. The right answer is more a comparison from one ligand's set of poses to another.
Q5: How do we cite the protein pulled from the RCSB database? Do we have to use [] at the end of the sentence? Does it have a (Company Name, City, State) citation as well? Where do we find the actual reference to put under our "References" section?
A: cite the paper that is associated with that PDB entry - e.g. is it he Cody, et al. paper for 1u72 Use standard ACS format for citing those. Yes - use the brackets to denote the citation number for that paper.
Q4: Do captions count in the word count?
A: No, captions do not count as the word count. Only the body of the report (appendix does not count and references section does not count)
Q3:
do I need an analysis at the end?
A:
yes - you need a brief overall analysis. How did the ligands do as a whole? And address error analysis. Address Precision and Accuracy directly.
Q2: for the analysis under each pair of pictures, should I just address the differences between the GOLD and Xray Crystallography figures, instead of answer the comparative: "compare this ligand to folate, ligand #2 and discuss differences in binding"?A:Keep these brief, but....yes - address differences between GOLD and xray pose,yes - make a statement about whether you think it binds better than the reference ligand (#2) - you will have already discussed differences in binding by answering the 1st part of this question.
Q1:for the methods, do we need to include the actual code that was changed between Parts 2 and 3, or can we just say tomodify the file such that 3 poses of each ligand are returned?A:actual code not needed, but say which 'parameter' was changed in the gold.conf
updated by Dr. B on 03/31/13 @ 10:21 PM
Q:
Q:
RESPONSES from Dr. B (or mentors)
Q19: On the analysis below each pair of images, what exactly do we need to discuss?
A: discuss the differences in the pose and the differences in estimated binding strength relative to what you see with regards to polar contacts and hydrophobic interactions. Also, state if it should be better or worse than the reference ligand (Folate #2)
Q18: Materials and Methods should be past tense right?
A: yes. M&M is past tense. (and pretty much everything else - unless it is future directions or the objective at the end of the intro)
Q17: When we need to site PyMol, GOLD, other instruments we used, do we need to always site the company, city, state/country every time it's mentioned or just the first time it's mentioned in our report?A: just the first time it is cited - usually in the M&M
Q16: Do we need figures 17 - 21 and 22/23 in our report? Those are decoy ligands and best/worst sets. They are not paired analysis of GOLD and x-ray data.
A: Yes - they are actually more interesting than the other images.
Q15: When citing GOLD, what is meant by the "first citation listed"? Is that the first reference on the pdf link for GOLD?----> [1] G. Jones, P.Willett, R. C. Glen, J. Mol. Biol., 245, 43-53, 1995; G. Jones, P.Willett, R. C. Glen, A. R. Leach, R. Taylor, J. Mol. Biol., 267, 727-748, 1997. ??A: yes - be sure to use ACS format though.
Q14: How can we group ligands that are similar in our analysis? Does this mean that we don"t have to talk about each pair of images after we show the pictures and just explain 4 images at once?A: Yes - it is permissible to talk about a 'set' of images if the ligand are very similar. The best case of this are the tautomers of deazafolate. They are very similar and can be discussed together for the analysis as to whether they match their crystal poses and whether they would be high affinity ligands based upon polar contacts and hydrophobic interactions. . But still need separate captions.
Q13: Does the introduction have to be around 500 words, because this takes up a large amount of the word limit? Is it okay if the introduction is around 300 words, so we can focus more on the analysis section?
A: It should be ~500 words. 400 is about as low as you should go.
Q14: I was wondering what "cite the PDB entry for your receptor" is asking for?
A: You want to cite the actual paper that the crystal structure is from (not just the PDB website page). Go to the page to find the artilcle http://www.rcsb.org/pdb/explore.do?structureId=1u72
(HINT: it was published in 2005) You can then get the full citation from PubMed or EndNote Web Online.
Q12: Can we use the comparisons that are in our lab analysis for our comparisons in the lab report? I planned on taking the answers in the lab analysis and making them more succint for the lab report. Is that okay?
A: yes - use your comparisons from the lab notebook and make them more succinct. Also, some ligands are very similar and can be grouped together in your analysis.
Q11: Should we put the excel table of both runs in our report or just the first one?
A: no - you really only need the 1st table.
Q10: I just realized that there were articles in the DDFE folder that we needed to save and keep for the lab report. Is there any way those could be uploaded to blackboard or to the VDS website so we can access them?
A: download WinSCP or SecureShell (from Bevoware on Utexas.edu) and remotely login to the DDFE.
Q9: Do the captions need to be in past tense as well or is it acceptable to have sentences such as "active site residues are shown as lines" "carbons on DHFR are colored green"?
A: no - it is best to keep those in present tense. 'active site residues shown as lines...."
Q8: Do all of the Figures from our notebook go into our report? Or are all twenty something figures too many to put in a lab report?
A: yes of the images listed should go in there (show the xray vs gold images side by side)
Q7: Should we capitalize things like "virtual screening" and "fitness score"? What about "hydrogen bond"?
A: 'Fitness Score' can be capitalized.
Q6: Since there is no way we can actually quanitfy the level of precision or accuracy that GOLD had, do we just use general adjectives based on our opinion/analysis? In short, is there a "right" answer?
A: correct - this is a more qualitative analysis. The right answer is more a comparison from one ligand's set of poses to another.
Q5: How do we cite the protein pulled from the RCSB database? Do we have to use [] at the end of the sentence? Does it have a (Company Name, City, State) citation as well? Where do we find the actual reference to put under our "References" section?
A: cite the paper that is associated with that PDB entry - e.g. is it he Cody, et al. paper for 1u72 Use standard ACS format for citing those. Yes - use the brackets to denote the citation number for that paper.
Q4: Do captions count in the word count?
A: No, captions do not count as the word count. Only the body of the report (appendix does not count and references section does not count)
Q3:
do I need an analysis at the end?
A:
yes - you need a brief overall analysis. How did the ligands do as a whole? And address error analysis. Address Precision and Accuracy directly.
Q2:
for the analysis under each pair of pictures, should I just address the differences between the GOLD and Xray Crystallography
figures, instead of answer the comparative: "compare this ligand to folate, ligand #2 and discuss differences in binding"?A:Keep these brief, but....yes - address differences between GOLD and xray pose,yes - make a statement about whether you think it binds better than the reference ligand (#2) - you will have already discussed differences in binding by answering the 1st part of this question.
Q1:for the methods, do we need to include the actual code that was changed between Parts 2 and 3, or can we just say tomodify the file such that 3 poses of each ligand are returned?A:actual code not needed, but say which 'parameter' was changed in the gold.conf